Changes in conformational dynamics of basic side chains upon protein-DNA association

Alexandre Esadze, Chuanying Chen, Levani Zandarashvili, Sourav Roy, Bernard Pettitt, Junji Iwahara

Research output: Contribution to journalArticle

33 Citations (Scopus)

Abstract

Basic side chains play major roles in recognition of nucleic acids by proteins. However, dynamic properties of these positively charged side chains are not well understood. In this work, we studied changes in conformational dynamics of basic side chains upon protein-DNA association for the zinc-finger protein Egr-1. By nuclear magnetic resonance (NMR) spectroscopy, we characterized the dynamics of all side-chain cationic groups in the free protein and in the complex with target DNA. Our NMR order parameters indicate that the arginine guanidino groups interacting with DNA bases are strongly immobilized, forming rigid interfaces. Despite the strong short-range electrostatic interactions, the majority of the basic side chains interacting with the DNA phosphates exhibited high mobility, forming dynamic interfaces. In particular, the lysine side-chain amino groups exhibited only small changes in the order parameters upon DNA-binding. We found a similar trend in the molecular dynamics (MD) simulations for the free Egr-1 and the Egr-1-DNA complex. Using the MD trajectories, we also analyzed side-chain conformational entropy. The interfacial arginine side chains exhibited substantial entropic loss upon binding to DNA, whereas the interfacial lysine side chains showed relatively small changes in conformational entropy. These data illustrate different dynamic characteristics of the interfacial arginine and lysine side chains.

Original languageEnglish (US)
Pages (from-to)6961-6970
Number of pages10
JournalNucleic Acids Research
Volume44
Issue number14
DOIs
StatePublished - Aug 19 2016

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DNA
Proteins
Lysine
Arginine
Entropy
Molecular Dynamics Simulation
Magnetic Resonance Spectroscopy
Zinc Fingers
Static Electricity
Nucleic Acids
Phosphates

ASJC Scopus subject areas

  • Genetics

Cite this

Changes in conformational dynamics of basic side chains upon protein-DNA association. / Esadze, Alexandre; Chen, Chuanying; Zandarashvili, Levani; Roy, Sourav; Pettitt, Bernard; Iwahara, Junji.

In: Nucleic Acids Research, Vol. 44, No. 14, 19.08.2016, p. 6961-6970.

Research output: Contribution to journalArticle

Esadze, Alexandre ; Chen, Chuanying ; Zandarashvili, Levani ; Roy, Sourav ; Pettitt, Bernard ; Iwahara, Junji. / Changes in conformational dynamics of basic side chains upon protein-DNA association. In: Nucleic Acids Research. 2016 ; Vol. 44, No. 14. pp. 6961-6970.
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